What we observed was that the people who had (free refill) cups to refill took them straight to the soda fountain area of the food line, and the workers would fill them in between customers in the food line. The cups we had cost 1.49 to refill, so we had to pay for the refill in line first, then go to the soda filling area of the line and hand them our receipt.
It worked out great for us...since we brought along a huge canteen sippy cup we bought 3 years ago at the Mummy ride, and it only cost 1.49 for refills.
So...if you have sippy cups from previous trips, bring them along!! We were glad we did!
I liked the idea of the free refill cups a lot...but when I saw how small they were, I was glad we had our Mummy canteen.
And hopefully you will be going to Universal at a time when the lines in general will be shorter.
I wish they had self serve refill stations too...but probably too many people would cheat the system that way.
Enjoy!